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Identifying stabilizing key residues in proteins using interresidue interaction energy matrix

SYSNO ASEP	0314780
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	Identifying stabilizing key residues in proteins using interresidue interaction energy matrix
Title	Identifikace klíčových reziduí pro stabilizaci proteinu použitím matice interakční energie
Author(s)	Biedermannová, Lada (UOCHB-X) Hobza, Pavel (UOCHB-X)_{RID, ORCID} Vondrášek, Jiří (UOCHB-X)_{RID, ORCID}
Source Title	Proteins-Structure, Function and Bioinformatics. - : Wiley - ISSN 0887-3585 Roč. 72, č. 1 (2008), s. 402-413
Number of pages	12 s.
Language	eng - English
Country	US - United States
Keywords	protein stabilisation ; an-initio calculation ; interaction energy
Subject RIV	CF - Physical ; Theoretical Chemistry
R&D Projects	GA203/05/0009 GA ČR - Czech Science Foundation (CSF)
	GA203/06/1727 GA ČR - Czech Science Foundation (CSF)
	GD203/05/H001 GA ČR - Czech Science Foundation (CSF)
	LC512 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
CEZ	AV0Z40550506 - UOCHB-X (2005-2011)
UT WOS	000256609800035
DOI	10.1002/prot.21938
Annotation	We are proposing an interresidue interaction energy map (IEM) – a new tool for protein structure analysis and protein bioinformatics. This approach employs the sum of pair-wise interaction energies of a particular residue as a measure of its structural importance. For the theoretical adjustment of the proposed method, we chose the Trp-cage mini protein as a model system to compare a spectrum of computational methods ranging from the ab initio MP2 level through the DFT method to empirical forcefield methods. The IEM method correctly identifies Tryptophane 6 as the key residue in the Trpcage. The other residues with the highest stabilizing contributions correspond to the structurally important positions in the protein.
Workplace	Institute of Organic Chemistry and Biochemistry
Contact	asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434
Year of Publishing	2009

Number of the records: 1